5FYR

Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, myoinositol complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FYP	PDB ENTRY 5FYP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10		PEG3350 24-27%, CAPS/BICINE MIX PH 9.0-10 GRID, BEST CRYSTALS CLOSER TO PH 10, SEEDING FROM PACT H4 (0.2M KSCN, 20% PEG3350, BIS TRIS PROPANE PH 8.5), ORYX ROBOT, 24 WELL PLATE, HANGING DROPS

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.443	α = 90
b = 135.443	β = 90
c = 113.732	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2015-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.45	48.93	99.7	0.07	14.5	7.2		184175		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47	95.2		0.6	2.5	5.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 5FYP	1.45	48.93	174938	9159	99.68	0.14722	0.14488	0.19184	RANDOM	16.818

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.07			-0.07		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.774
r_sphericity_free	27.31
r_dihedral_angle_4_deg	16.4
r_dihedral_angle_3_deg	11.608
r_sphericity_bonded	9.027
r_dihedral_angle_1_deg	6.327
r_rigid_bond_restr	4.143
r_long_range_B_refined	3.962
r_long_range_B_other	3.925
r_scangle_other	3.216
r_scbond_it	2.708
r_scbond_other	2.708
r_mcangle_other	2.146
r_mcangle_it	2.145
r_mcbond_it	1.877
r_mcbond_other	1.876
r_angle_refined_deg	1.666
r_angle_other_deg	1.101
r_chiral_restr	0.468
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9065
Nucleic Acid Atoms
Solvent Atoms	1072
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing